We'll need specific examples of the game and what did and didn't download in order to look into this.
In theory, there shouldn't ever be a case where the region's proper title doesn't match the title on the ROM file, but perhaps that is a possibility. Currently we use the name that matches the region on the ROM file as priority #1. We're going to change that for the next beta to use the title on the ROM file as priority #1 instead, and then the region title.
I have not heard of these issues elsewhere at this point. I'll do some testing with Refried though to see if it's a theme-specific issue. Also could be plugin-related, so if you have any plugins, try removing them (and let us know which ones are causing issues).